.compute_cell_auc       Compute AUC for a single cell
.ensure_genes_x_cells_format
                        Validate expression matrix is in genes x cells
                        format
AUCProcessor            Initialize AUCProcessor
AUCProcessor-class      AUCProcessor class
SimiCvizExperiment      Construct a SimiCvizExperiment object
SimiCvizExperiment-class
                        SimiCvizExperiment class
auc_list_to_df          Collect per-label AUC matrices using cell
                        labels
calculate_activity_scores
                        Calculate activity scores from
                        SimiCvizExperiment weights
calculate_dissimilarity
                        Calculate dissimilarity scores across phenotype
                        labels
calculate_ecdf_auc      Calculate ECDF AUC
compute_auc             Compute activity scores for an object
compute_auc,AUCProcessor-method
                        Compute activity scores for all cells
export_SimiCviz_csv     Export SimiCvizExperiment tables to CSV
get_auc                 Extract activity scores from an object
get_auc,AUCProcessor-method
                        Get computed activity scores
get_tf_network          Extract stacked TF-target weight matrix across
                        labels
is.SimiCvizExperiment   Check if object is a SimiCvizExperiment
load_SimiCPipeline      Create a SimiCvizExperiment from SimiCPipeline
                        output path
load_cell_labels        Load cell-to-label mapping
load_collected_auc      Load a collected AUC CSV into a data.frame
load_expression_matrix
                        Load expression matrix from various sources
                        /file formats Allowed formats: • CSV file •
                        h5ad file • rds file (Seurat or
                        SingleCellExperiment object) • matrix or
                        data.frame in R
load_from_csv           Create a SimiCvizExperiment from CSV files
plot_auc_cumulative     Plot AUC cumulative (ECDF) curves by label
plot_auc_distributions
                        Plot AUC density distributions by label
plot_auc_heatmap        Plot mean AUC heatmap by TF and label
plot_auc_summary_statistics
                        Plot AUC summary statistics
plot_dissimilarity_heatmap
                        Plot dissimilarity heatmap
plot_r2_distribution    Plot adjusted R² distributions
plot_target_weights     Plot weight barplots for target genes
plot_tf_network_heatmap
                        Plot heatmap of a TF regulatory network across
                        phenotypes
plot_tf_weights         Plot weight barplots for transcription factors
read_auc_csv            Read SimiC-style AUC results from CSV
                        (compatibility)
read_auc_pickle         Read SimiCPipeline output AUC matrices (pickle
                        file)
read_pickle             Read pickle files
read_weights_csv        Read Long-style TF-target weights from CSV
                        (compatibility)
read_weights_pickle     Read SimiCPipeline output weights (pickle file)
setCellLabels           Set or update cell-to-label mapping
setLabelNames           Set or update label names and colors
